X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=75a5c9cd32bace353f9e504c84b7ecb72d0de62b;hb=71fc0e8716067e0d1100f82cced73c38bfb8d7f6;hp=fc12b3bdbbd6b43c4fe346d1e707c418bab4798e;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
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@@ -1,59 +1,88 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
Viewing PDB Structures
++ Jalview can view protein structures associated with a sequence via the + "Structure→" submenu from a sequence's pop-up menu. +
+ The + Jmol viewer has been included since Jalview + 2.3. Jalview 2.8.2 included support for + Chimera, provided it is + installed and can be launched by Jalview. The default viewer can be + configured in the + Structure tab in the + Tools→Preferences dialog box. ++ Structure data imported into Jalview can also be processed to display + secondary structure and temperature factor annotation. See the Annotation from Structure page for + more information. +
+The following menu entries are provided for viewing structure data
+
Jalview can view protein structures associated with a sequence -via the "Structure→View PDB entry:" entries from a -sequence's pop-up menu. Once a pdb +
If a single pdb structure is selected, one of the following will happen:
- Opening structures associated with the current selection
- If one or more of the sequences in the alignment are selected, then
- the Structure submenu of the Sequence
- ID popup menu will contain will include either a 'View all X
- structures' entry in the submenu or a 'View structure for Sequence'
- entry. Both these options will open a new Jmol view containing one, or
- all the structures available for all selected sequences, superimposed
- using the currently selected region of the alignment. (This
- capability was added in Jalview 2.7)
-
Associating PDB files with Sequences
To associate PDB files with a sequence, right click on a sequence ID and select "Structure→ Associate Structure with